Yes, in fact the river logs killed Nuka. But Zira blamed Kovu for it, because if Kovu had catched Simba, then Nuka wouldn't have gone to catch Simba, and the logs wouldn't have crushed Nuka. In other words, in Zira's view, Kovu was responsible for Nuka's death.

I'm pretty sure it's due to the fact Kovu rejected to step into the fights and retreated away, causing inexperienced Nuka to try and take his place, ultimately result9in his death. If Kovu had stepped in, Nuka would not have taken his actions.

It was the log that actually killed Nuka, but Zira was calling Kovu a coward for not killing Simba so therefore he "caused" Nuka's death. People blame others a lot for a death after the fact as hindsight is 20/20. Parents who lose children in accidental deaths such as pool drownings say "Well, if you had been watching him/her they wouldn't have died!"

He indirectly killed Nuka, and I think was angry with Kovu already since didn't want to kill Simba, so she tried to make him think that his decision not to kill Simba had lead to the death of a close one.

Obviously, Kovu didn't kill Nuka, and it's not Kovu's fault that Nuka recklessly chased Simba up the log pile. If anyone's to blame for Nuka's death, it's Zira. But Zira would never admit that she's to blame, and wrongfully placed the blame on Kovu since she resented him for not killing Simba. Which is a very realistic reaction, to be quite frank, as people more often than not are quick to blame everyone but themselves. Really humanizes Zira.